The purpose of this application is to leverage our Illumina Genome Analyzer IIx (GAIIx) next generation sequencer asset to upgrade and better serve the deep sequencing needs of investigators within the Lerner Research Institute and the research enterprise of the Cleveland Clinic Health System by requesting funds to purchase the higher throughput, flexible, state-of-the-art, Illumina HiSeq2500 instrument system. The HiSeq2500 instrument is the latest in the Illumina suite of massively parallel sequencing instruments developed as a direct consequence of the NIH initiative for the $1,000 genome project. It has a higher sequence read output, a rapid-run mode for greater flexibility enabling a wider range of genome-scale applications while being more cost effective to run than the GAIIx. The HiSeq2500 represents the most versatile, in terms of applications capabilities, of the Illumina instruments and technologies to come to the market. The underlying technology can be summarized as massively parallel sequencing using bead-based flowcells with single base synthesis TruSeq v3 chemistry (maximum output 600 Gb of sequence in a typical 10 day high throughput run). As detailed in the application, the instrument and technology will support our projects that primarily include biomarker discovery, transcriptome, methylome, metagenome and clinical/translational studies that represent the unique strengths of our institution. The projects will take advantage of the HiSeq2500 advances of scale, versatility and higher sample multiplexing capability. Higher numbers of output reads per flowcell than the GAIIx leads to higher library multiplexing capability for RNA-seq resulting in less expense per sample, better dynamic range than microarray profiling, the ability to reliably detect low- abundance transcripts and to discover novel transcripts for whole transcriptome, small or non-coding RNA discovery and gene expression profiling. The HiSeq2500 takes less time to complete genome- wide profiles of DNA-protein regulatory interactions, epigenetic regulation, whole genome sequencing, exome sequencing, re-sequencing of large genomic regions in translational research with patient DNA to uncover human disease causing mutations and translational metagenomic studies of human gut flora. The HiSeq2500 is essential to lift the current NIH-funded projects to the next level and to seed new endeavors in northeast Ohio. Cleveland Clinic has already committed substantial resources to the development of translational genomics and genomic medicine by founding the LRI-Genomics Core within the Genomic Medicine Institute and by supporting its operation within the larger Research Core Services infrastructure to ensure its operation and maintenance for the long-term.